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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $species_info = array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ) $local_species = 'cbr' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $species_info = array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ) $local_species = 'cre' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $species_info = array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ) $local_species = 'ugi' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $species_info = array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ) $local_species = 'vma' $disabled = '' $selected = '' $num_hits = (int) 1
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ), 'gf_id' => 'HOM05D001103', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001103' ), 'data_identifier' => 'HOM05D001103', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001103', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '555', 'num_species' => '98' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p20170' => 'bna', 'A03p50360' => 'bna', 'A06p10880' => 'bna', 'A06p44070' => 'bna', 'A07p12410' => 'bna', 'A07p23390' => 'bna', 'A07p32180' => 'bna', 'A07p34560' => 'bna', 'A08p26770' => 'bna', 'A09p39030' => 'bna', 'A09p61760' => 'bna', 'Aa31LG2G8140' => 'aar', 'Aa31LG6G40' => 'aar', 'Aa31LG7G9340' => 'aar', 'Aa31LG7G9360' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_340.162' => 'aag', 'Actinidia01828' => 'ach', 'Actinidia02290' => 'ach', 'Actinidia02291' => 'ach', 'Actinidia12397' => 'ach', 'Actinidia17953' => 'ach', 'Actinidia26835' => 'ach', 'Actinidia26836' => 'ach', 'Actinidia36623' => 'ach', 'Actinidia38439' => 'ach', 'Ah.02g127890' => 'amhyb', 'Ah.03g137190' => 'amhyb', 'Ah.04g150910' => 'amhyb', 'AL1G26860' => 'aly', 'AL1G32095' => 'aly', 'AL1G40210' => 'aly', 'AL2G26850' => 'aly', 'AL5G10870' => 'aly', 'AL7G37490' => 'aly', 'Aqoxy1G00390' => 'aox', 'Aqoxy3G00025' => 'aox', 'Aqoxy3G04070' => 'aox', 'Aqoxy4G02254' => 'aox', 'arahy.Tifrunner.gnm1.ann1.0MAX30' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.31M0G5' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.8JYA65' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B43GKP' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.E2679H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H20A63' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.HHC45T' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ID7VTD' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JUDK08' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P0XMJJ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.PTXY5H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Z0CS2Z' => 'arhy', 'AT1G14840' => 'ath', 'AT1G24764' => 'ath', 'AT1G68060' => 'ath', 'AT2G01750' => 'ath', 'AT4G17220' => 'ath', 'ATR0753G014' => 'atr', 'ATR0796G322' => 'atr', 'ATR0827G114' => 'atr', 'ATR1096G123' => 'atr', 'Atru.chr1.1435' => 'acertr', 'Atru.chr1.2301_Atru.chr1.2302' => 'acertr', 'Atru.chr1.2305' => 'acertr', 'Atru.chr1.2306' => 'acertr', 'Atru.chr11.915' => 'acertr', 'AUR62012836' => 'cqu', 'AUR62014148' => 'cqu', 'AUR62018351' => 'cqu', 'AUR62021823' => 'cqu', 'AUR62024351' => 'cqu', 'AUR62030315' => 'cqu', 'AUR62038491' => 'cqu', 'BcaB02g06553' => 'bca', 'BcaB03g12043' => 'bca', 'BcaB03g14020' => 'bca', 'BcaB03g15135' => 'bca', 'BcaB03g15396' => 'bca', 'BcaB03g15397' => 'bca', 'BcaB04g17921' => 'bca', 'BcaB04g18763' => 'bca', 'BcaC01g01668' => 'bca', 'BcaC01g02584' => 'bca', 'BcaC02g09213' => 'bca', 'BcaC05g25405' => 'bca', 'BcaC05g26497' => 'bca', 'BcaC05g26696' => 'bca', 'BcaC06g31280' => 'bca', 'BcaC06g33548' => 'bca', 'BcaC06g34123' => 'bca', 'BcaC06g35240' => 'bca', 'BcaC06g35241' => 'bca', 'BcaC07g41535' => 'bca', 'BcaC08g45233' => 'bca', 'BcaC08g46001' => 'bca', 'BcaC08g46233' => 'bca', 'BcaC09g50450' => 'bca', 'BcaC09g51389' => 'bca', 'BcaNung00111' => 'bca', 'BcaNung03471' => 'bca', 'BcaNung04322' => 'bca', 'BolC1t02479H' => 'bol', 'BolC3t18576H' => 'bol', 'BolC3t19620H' => 'bol', 'BolC4t25587H' => 'bol', 'BolC4t25588H' => 'bol', 'BolC5t30027H' => 'bol', 'BolC5t31276H' => 'bol', 'BolC6t38894H' => 'bol', 'BolC6t39232H' => 'bol', 'BolC7t42344H' => 'bol', 'BolC7t43775H' => 'bol', 'BolC7t45374H' => 'bol', 'BolC8t52092H' => 'bol', 'BraA01t01940Z' => 'bra', 'BraA03t14125Z' => 'bra', 'BraA06t24266Z' => 'bra', 'BraA06t27281Z' => 'bra', 'BraA07t29021Z' => 'bra', 'BraA07t30848Z' => 'bra', 'BraA08t34622Z' => 'bra', 'BraA09t39403Z' => 'bra', 'BraA09t41546Z' => 'bra', 'C01p25290' => 'bna', 'C03p63210' => 'bna', 'C03p63220' => 'bna', 'C03p63230' => 'bna', 'C03p73230' => 'bna', 'C04p40110' => 'bna', 'C04p40120' => 'bna', 'C05p12820' => 'bna', 'C05p25480' => 'bna', 'C06p37950' => 'bna', 'C06p41970' => 'bna', 'C07p18340' => 'bna', 'C07p32390' => 'bna', 'C07p48670' => 'bna', 'C08p45370' => 'bna', 'CAN.G1156.9' => 'can', 'CAN.G1263.27' => 'can', 'CAN.G1986.9' => 'can', 'CAN.G282.132' => 'can', 'CAN.G74.16' => 'can', 'CANSAT01G3129' => 'cansat', 'CANSAT56G0682' => 'cansat', 'CANSAT64G0173' => 'cansat', 'CARHR015380' => 'chi', 'CARHR026370' => 'chi', 'CARHR035600' => 'chi', 'CARHR056110' => 'chi', 'CARHR056160' => 'chi', 'CARHR060720' => 'chi', 'CARHR144320' => 'chi', 'CARHR223830' => 'chi', 'CARHR258900' => 'chi', 'CARHR284510' => 'chi', 'Carub.0001s1463' => 'cru', 'Carub.0001s2540' => 'cru', 'Carub.0002s1454' => 'cru', 'Carub.0005s0070' => 'cru', 'Carub.0007s2419' => 'cru', 'Ca_00752_v3' => 'car', 'Ca_12537_v3' => 'car', 'Ca_12545_v3' => 'car', 'Ca_17274_v3' => 'car', 'Ca_21000_v3' => 'car', 'Ca_23394_v3' => 'car', 'CBR_g4681' => 'cbr', 'Cc06_g19370' => 'ccan', 'Cc06_g19380' => 'ccan', 'Cc09_g00490' => 'ccan', 'Cc09_g00500' => 'ccan', 'Cc11_g07390' => 'ccan', 'CDE04G3473' => 'cde', 'CDE05G2989' => 'cde', 'CDE06G1332' => 'cde', 'CDE11G0397' => 'cde', 'Cfa000048' => 'cfa', 'Cfa015026' => 'cfa', 'Ciclev10014625m.g' => 'ccl', 'Ciclev10014697m.g' => 'ccl', 'CiPaw.05G188900' => 'cil', 'CiPaw.06G052400' => 'cil', 'CiPaw.09G048100' => 'cil', 'CiPaw.09G107700' => 'cil', 'CiPaw.10G080600' => 'cil', 'CiPaw.10G080900' => 'cil', 'ClCG01G021290' => 'cla', 'ClCG04G005550' => 'cla', 'ClCG04G005560' => 'cla', 'ClCG07G005600' => 'cla', 'COL.COLO4_16598' => 'col', 'COL.COLO4_16599' => 'col', 'COL.COLO4_31925' => 'col', 'COL.COLO4_37448' => 'col', 'Cpa.g.sc2.189' => 'cpa', 'Cpa.g.sc27.245' => 'cpa', 'Cre14.g618150' => 'cre', 'CsaV3_4G029590' => 'csa', 'CsaV3_5G015790' => 'csa', 'CsaV3_6G048290' => 'csa', 'CSS0018064' => 'camsi', 'CSS0018869' => 'camsi', 'CSS0026312' => 'camsi', 'CSS0027324' => 'camsi', 'DCAR_002237' => 'dca', 'DCAR_007332' => 'dca', 'DCAR_016881' => 'dca', 'DCAR_023575' => 'dca', 'DCAR_026804' => 'dca', 'Dinv04402' => 'din', 'Dinv06173' => 'din', 'Dinv06174' => 'din', 'Dinv07724' => 'din', 'Dinv10470' => 'din', 'Dinv12040' => 'din', 'Dinv15360' => 'din', 'Duzib106G1209' => 'dzi', 'Duzib192G0471' => 'dzi', 'Duzib235G0778' => 'dzi', 'Duzib248G0174' => 'dzi', 'Duzib251G0121' => 'dzi', 'Duzib268G1612' => 'dzi', 'ECA233G3874' => 'eca', 'ECA234G0551' => 'eca', 'ECA234G2924' => 'eca', 'ECA240G1673' => 'eca', 'ECA246G4154' => 'eca', 'ECA248G2423' => 'eca', 'EL10Ac3g07241' => 'bvu', 'EL10Ac6g14199' => 'bvu', 'EL10Ac8g20252' => 'bvu', 'Eucgr.A02239' => 'egr', 'Eucgr.B02673' => 'egr', 'Eucgr.E03882' => 'egr', 'FAN07G0112' => 'fan', 'FAN12G2518' => 'fan', 'FAN17G1462' => 'fan', 'FAN21G2597' => 'fan', 'FAN22G0254' => 'fan', 'FAN25G0822' => 'fan', 'FvH4_3g00480' => 'fve', 'FvH4_4g33511' => 'fve', 'Glyma.02G085500' => 'gma', 'Glyma.03G127500' => 'gma', 'Glyma.05G239100' => 'gma', 'Glyma.07G170700' => 'gma', 'Glyma.07G267400' => 'gma', 'Glyma.08G046200' => 'gma', 'Glyma.09G013100' => 'gma', 'Glyma.15G118000' => 'gma', 'Glyma.17G006600' => 'gma', 'Glyma.19G130100' => 'gma', 'Gohir.A01G146400' => 'ghi', 'Gohir.A04G143000' => 'ghi', 'Gohir.A05G175700' => 'ghi', 'Gohir.A05G308700' => 'ghi', 'Gohir.A06G154800' => 'ghi', 'Gohir.A12G152200' => 'ghi', 'Gohir.D01G139600' => 'ghi', 'Gohir.D04G186300' => 'ghi', 'Gohir.D05G178800' => 'ghi', 'Gohir.D05G309400' => 'ghi', 'Gohir.D06G162700' => 'ghi', 'Gohir.D12G155666' => 'ghi', 'Gohir.D12G155732' => 'ghi', 'Gorai.002G171800' => 'gra', 'Gorai.008G168300' => 'gra', 'Gorai.009G184200' => 'gra', 'Gorai.009G329800' => 'gra', 'Gorai.010G189900' => 'gra', 'Gorai.012G182700' => 'gra', 'GSVIVG01003492001' => 'vvi', 'GSVIVG01011656001' => 'vvi', 'GSVIVG01033637001' => 'vvi', 'HanXRQChr01g0008221' => 'han', 'HanXRQChr12g0364961' => 'han', 'HanXRQChr12g0375481' => 'han', 'HanXRQChr13g0388251' => 'han', 'HanXRQChr15g0480271' => 'han', 'HanXRQChr16g0516401' => 'han', 'HanXRQChr16g0527311' => 'han', 'HanXRQChr17g0566421' => 'han', 'Haze_07005' => 'cav', 'Haze_10871' => 'cav', 'Haze_20231' => 'cav', 'Hma1.2p1_0277F.1_g111650' => 'hma', 'Hma1.2p1_0548F.1_g176760' => 'hma', 'Hma1.2p1_0940F.1_g239560' => 'hma', 'Hma1.2p1_1963F.1_g309300' => 'hma', 'HPP92_002296' => 'vpl', 'HPP92_006040' => 'vpl', 'HPP92_010025' => 'vpl', 'HPP92_010980' => 'vpl', 'HPP92_013122' => 'vpl', 'HPP92_015297' => 'vpl', 'HPP92_020451' => 'vpl', 'HPP92_020484' => 'vpl', 'Hund19092' => 'sun', 'Hund21136' => 'sun', 'Hund24584' => 'sun', 'Hund24930' => 'sun', 'Lalb_Chr04g0258681' => 'lal', 'Lalb_Chr05g0222191' => 'lal', 'Lalb_Chr09g0330851' => 'lal', 'Lalb_Chr10g0095681' => 'lal', 'Lalb_Chr14g0365801' => 'lal', 'Lalb_Chr16g0387511' => 'lal', 'Lalb_Chr17g0338431' => 'lal', 'Lalb_Chr18g0057171' => 'lal', 'Lalb_Chr22g0357451' => 'lal', 'Lalb_Chr22g0357461' => 'lal', 'Lalb_Chr25g0281421' => 'lal', 'Lj1g0022653' => 'lja', 'Lj2C258T10' => 'lonja', 'Lj2g0004872' => 'lja', 'Lj4g0011451' => 'lja', 'Lj4g0015594' => 'lja', 'Lj6C737T13' => 'lonja', 'Lj6g0025885' => 'lja', 'Lsat_1_v5_gn_3_105980' => 'lsa', 'Lsat_1_v5_gn_4_24841' => 'lsa', 'Lsat_1_v5_gn_4_63560' => 'lsa', 'Lsat_1_v5_gn_5_157060' => 'lsa', 'Lsat_1_v5_gn_8_117881' => 'lsa', 'Lsat_1_v5_gn_8_35461' => 'lsa', 'Manes.08G060700' => 'mes', 'Manes.08G070200' => 'mes', 'Manes.09G078100' => 'mes', 'Manes.15G134400' => 'mes', 'Manes.17G084100' => 'mes', 'Mapoly0041s0116' => 'mpo', 'MBI13_g24901_MAGBIO' => 'mbi', 'MBI16_g22431_MAGBIO' => 'mbi', 'MBI18_g03870_MAGBIO' => 'mbi', 'MBI19_g36137_MAGBIO' => 'mbi', 'MBI19_g44855_MAGBIO' => 'mbi', 'MD00G1056800' => 'mdo', 'MD00G1075100' => 'mdo', 'MD12G1095700' => 'mdo', 'MD13G1020100' => 'mdo', 'MD16G1018200' => 'mdo', 'Medtr1g032520' => 'mtr', 'Medtr2g026590' => 'mtr', 'Medtr4g133890' => 'mtr', 'Medtr8g021120' => 'mtr', 'Medtr8g105350' => 'mtr', 'MELO3C016657.2' => 'cme', 'MELO3C019083.2' => 'cme', 'Migut.E00485' => 'egut', 'Migut.J01651' => 'egut', 'Migut.M01437' => 'egut', 'MSTRG.13628' => 'ama', 'MSTRG.16045' => 'ama', 'MSTRG.19801' => 'ama', 'MSTRG.6370' => 'ama', 'Nitab4.5_0000069g0260' => 'nta', 'Nitab4.5_0000069g0270' => 'nta', 'Nitab4.5_0000147g0280' => 'nta', 'Nitab4.5_0000198g0150' => 'nta', 'Nitab4.5_0000282g0060' => 'nta', 'Nitab4.5_0001668g0080' => 'nta', 'Nitab4.5_0002803g0030' => 'nta', 'Nitab4.5_0003871g0070' => 'nta', 'Nitab4.5_0004646g0050' => 'nta', 'Nitab4.5_0008786g0010' => 'nta', 'Nitab4.5_0011751g0010' => 'nta', 'Nn1g03203' => 'nnu', 'Nn1g09771' => 'nnu', 'Nn2g14701' => 'nnu', 'Nn3g18378' => 'nnu', 'Nn4g24398' => 'nnu', 'Nn7g36787' => 'nnu', 'Oeu031612.1' => 'oeu', 'Oeu044007.1' => 'oeu', 'Oeu047046.3' => 'oeu', 'Oeu052844.3' => 'oeu', 'Oeu052863.3' => 'oeu', 'Oeu057026.6' => 'oeu', 'Oeu059353.1' => 'oeu', 'Oeu059521.1' => 'oeu', 'Oeu062638.1' => 'oeu', 'Os03g0215700' => 'osa', 'Os06g0251700' => 'osa', 'Os12g0640900' => 'osa', 'Peaxi162Scf00008g00212' => 'pax', 'Peaxi162Scf00044g01821' => 'pax', 'Peaxi162Scf00047g02460' => 'pax', 'Peaxi162Scf00076g00422' => 'pax', 'Peaxi162Scf00655g00121' => 'pax', 'Peaxi162Scf00937g00328' => 'pax', 'Peaxi162Scf01544g00022' => 'pax', 'PGR031G2998' => 'pgr', 'PGR042G3059' => 'pgr', 'PGR102G0908' => 'pgr', 'PGSC0003DMG400015004' => 'stu', 'PGSC0003DMG400019974' => 'stu', 'PGSC0003DMG400021781' => 'stu', 'PGSC0003DMG400029515' => 'stu', 'PGSC0003DMG401013295' => 'stu', 'PGSC0003DMG401014948' => 'stu', 'PGSC0003DMG402014948' => 'stu', 'Phvul.001G123200' => 'pvu', 'Phvul.002G321500' => 'pvu', 'Phvul.003G018100' => 'pvu', 'Phvul.003G086000' => 'pvu', 'Phvul.005G021300' => 'pvu', 'Phvul.006G140300' => 'pvu', 'Phvul.010G075840' => 'pvu', 'Potri.006G018000' => 'ptr', 'Potri.006G039200' => 'ptr', 'Potri.008G135100' => 'ptr', 'Potri.010G106100' => 'ptr', 'Potri.016G006900' => 'ptr', 'Potri.016G036300' => 'ptr', 'Pp3c11_23600' => 'ppa', 'Pp3c18_2630' => 'ppa', 'Pp3c18_2960' => 'ppa', 'Pp3c18_2990' => 'ppa', 'Pp3c18_3000' => 'ppa', 'Pp3c21_20100' => 'ppa', 'Pp3c21_20150' => 'ppa', 'Pp3c23_7500' => 'ppa', 'Pp3c7_2540' => 'ppa', 'Pp3s177_60' => 'ppa', 'Prupe.1G333700' => 'ppe', 'Prupe.4G005400' => 'ppe', 'Prupe.7G032400' => 'ppe', 'Prupe.7G032700' => 'ppe', 'Prupe.7G033200' => 'ppe', 'Psat1g174280' => 'psa', 'Psat4g002440' => 'psa', 'Psat4g168560' => 'psa', 'Psat6g046640' => 'psa', 'Psat7g007800' => 'psa', 'PSO017G0044' => 'pso', 'PSO478G2239' => 'pso', 'PSO541G5050' => 'pso', 'PSO675G3477' => 'pso', 'QL03p036025' => 'qlo', 'QL05p068135' => 'qlo', 'QL07p010964' => 'qlo', 'QL07p010987' => 'qlo', 'QL07p011005' => 'qlo', 'QL11p052605' => 'qlo', 'RcHm_v2.0_Chr3g0480111' => 'rch', 'RcHm_v2.0_Chr4g0443021' => 'rch', 'RcHm_v2.0_Chr5g0000651' => 'rch', 'Rhsim09G0089200' => 'rsi', 'Rhsim13G0142100' => 'rsi', 'Sabra03G0000700' => 'sbr', 'Sabra05G0005500' => 'sbr', 'Sabra06G0013100' => 'sbr', 'Sabra06G0026400' => 'sbr', 'Sabra08G0103000' => 'sbr', 'Sabra10G0074800' => 'sbr', 'Sabra14G0144500' => 'sbr', 'Sabra16G0011800' => 'sbr', 'Sabra16G0038400' => 'sbr', 'Sabra17G0030900' => 'sbr', 'SalBow2G1514' => 'sbo', 'SalBow6G2831' => 'sbo', 'SalBow8G1018' => 'sbo', 'Sc05g0009790' => 'sci', 'Sc14g0006570' => 'sci', 'Sc19g0008140' => 'sci', 'Sc19g0008150' => 'sci', 'Sc25g0005450' => 'sci', 'Sed0000441' => 'sed', 'Sed0002320' => 'sed', 'Sed0004797' => 'sed', 'Sed0009793' => 'sed', 'Sed0013639' => 'sed', 'SEGI_28991' => 'sgi', 'SEGI_32507' => 'sgi', 'SEGI_41138' => 'sgi', 'SGA_v2.0_scaffold131G34407' => 'sas', 'SGA_v2.0_scaffold151G36785' => 'sas', 'SGA_v2.0_scaffold23G10198' => 'sas', 'SGA_v2.0_scaffold42G16192' => 'sas', 'SGA_v2.0_scaffold69G23154' => 'sas', 'SGA_v2.0_scaffold6G03250' => 'sas', 'SGA_v2.0_scaffold75G24778' => 'sas', 'SGA_v2.0_scaffold7G03704' => 'sas', 'SHI04308' => 'shi', 'SMO364G0775' => 'smo', 'Solyc01g005330.3' => 'sly', 'Solyc04g008040.4' => 'sly', 'Solyc04g015010.4' => 'sly', 'Solyc05g017980.3' => 'sly', 'Solyc11g012660.2' => 'sly', 'Solyc12g021250.3' => 'sly', 'Solyc12g021260.1' => 'sly', 'Sopen01g001350' => 'spe', 'Sopen04g003190' => 'spe', 'Sopen04g007030' => 'spe', 'Sopen05g014550' => 'spe', 'Sopen11g007390' => 'spe', 'Sp1g13280' => 'spa', 'Sp1g23090' => 'spa', 'Sp2g13200' => 'spa', 'Sp5g23060' => 'spa', 'Sp7g16970' => 'spa', 'TAR365G0286' => 'tar', 'TAR369G1089' => 'tar', 'TAR371G0083' => 'tar', 'TAR374G0809' => 'tar', 'TAR622G1427' => 'tar', 'TAR626G0007' => 'tar', 'TAR626G1305' => 'tar', 'TAR626G1561' => 'tar', 'TAR629G0434' => 'tar', 'THA.LOC104800010' => 'tha', 'THA.LOC104807931' => 'tha', 'THA.LOC104812799' => 'tha', 'THA.LOC104821905' => 'tha', 'THA.LOC104823667' => 'tha', 'THA.LOC104824127' => 'tha', 'Thecc.02G293300' => 'tca', 'Thecc.05G129700' => 'tca', 'Thecc.06G238600' => 'tca', 'Thhalv10003816m.g' => 'esa', 'Thhalv10007068m.g' => 'esa', 'Thhalv10007120m.g' => 'esa', 'Thhalv10018271m.g' => 'esa', 'Thhalv10024950m.g' => 'esa', 'TPR.G10586' => 'tpr', 'TPR.G10601' => 'tpr', 'TPR.G16757' => 'tpr', 'TPR.G19251' => 'tpr', 'TPR.G1957' => 'tpr', 'TPR.G36957' => 'tpr', 'TPR.G5955' => 'tpr', 'TWI38G1918' => 'twi', 'TWI63G1352' => 'twi', 'TWI74G1136' => 'twi', 'TWI74G1432' => 'twi', 'TWI77G0007' => 'twi', 'TWI77G0960' => 'twi', 'unitig_0.g605' => 'ugi', 'unitig_22.g6329' => 'ugi', 'unitig_60.g25477' => 'ugi', 'unitig_699.g19541' => 'ugi', 'unitig_8.g3082' => 'ugi', 'vmacro00551' => 'vma', 'vmacro03620' => 'vma', 'vmacro07789' => 'vma', 'vmacro10696' => 'vma', 'VMungo0251G1830' => 'vmu', 'VMungo0540G1190' => 'vmu', 'VMungo1215G2353' => 'vmu', 'VMungo1383G3626' => 'vmu', 'Zm00001eb008710' => 'zma', 'Zm00001eb133890' => 'zma', 'Zm00001eb253850' => 'zma', 'Zm00001eb280250' => 'zma', 'Zm00001eb371500' => 'zma' ) $gf_id = 'HOM05D001103' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001103' ) $data_identifier = 'HOM05D001103' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 26, 'aar' => (int) 4, 'aag' => (int) 1, 'ach' => (int) 9, 'amhyb' => (int) 3, 'aly' => (int) 6, 'aox' => (int) 4, 'arhy' => (int) 12, 'ath' => (int) 5, 'atr' => (int) 4, 'acertr' => (int) 5, 'cqu' => (int) 7, 'bca' => (int) 28, 'bol' => (int) 13, 'bra' => (int) 9, 'can' => (int) 5, 'cansat' => (int) 3, 'chi' => (int) 10, 'cru' => (int) 5, 'car' => (int) 6, 'cbr' => (int) 1, 'ccan' => (int) 5, 'cde' => (int) 4, 'cfa' => (int) 2, 'ccl' => (int) 2, 'cil' => (int) 6, 'cla' => (int) 4, 'col' => (int) 4, 'cpa' => (int) 2, 'cre' => (int) 1, 'csa' => (int) 3, 'camsi' => (int) 4, 'dca' => (int) 5, 'din' => (int) 7, 'dzi' => (int) 6, 'eca' => (int) 6, 'bvu' => (int) 3, 'egr' => (int) 3, 'fan' => (int) 6, 'fve' => (int) 2, 'gma' => (int) 10, 'ghi' => (int) 13, 'gra' => (int) 6, 'vvi' => (int) 3, 'han' => (int) 8, 'cav' => (int) 3, 'hma' => (int) 4, 'vpl' => (int) 8, 'sun' => (int) 4, 'lal' => (int) 11, 'lja' => (int) 5, 'lonja' => (int) 2, 'lsa' => (int) 6, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 5, 'mdo' => (int) 5, 'mtr' => (int) 5, 'cme' => (int) 2, 'egut' => (int) 3, 'ama' => (int) 4, 'nta' => (int) 11, 'nnu' => (int) 6, 'oeu' => (int) 9, 'osa' => (int) 3, 'pax' => (int) 7, 'pgr' => (int) 3, 'stu' => (int) 7, 'pvu' => (int) 7, 'ptr' => (int) 6, 'ppa' => (int) 10, 'ppe' => (int) 5, 'psa' => (int) 5, 'pso' => (int) 4, 'qlo' => (int) 6, 'rch' => (int) 3, 'rsi' => (int) 2, 'sbr' => (int) 10, 'sbo' => (int) 3, 'sci' => (int) 5, 'sed' => (int) 5, 'sgi' => (int) 3, 'sas' => (int) 8, 'shi' => (int) 1, 'smo' => (int) 1, 'sly' => (int) 7, 'spe' => (int) 5, 'spa' => (int) 5, 'tar' => (int) 9, 'tha' => (int) 6, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 7, 'twi' => (int) 6, 'ugi' => (int) 5, 'vma' => (int) 4, 'vmu' => (int) 4, 'zma' => (int) 5 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb371500' $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